A great breakfast place in San Rafael is Pier 15. New owners last year improved the food (especially breakfasts). The front of the place is "old bar" and the rear a bright, sunny dining room plus deck looking out on a somewhat seedy San Rafael boat scene. Here's a discussion from early this year: http://www.chowhound.com/topics/356004

Wish I'd seen this earlier, as I just got back from Mendo and my usual breakfast stop on the way - Horn of Zeese in Boonville - has been converted into a mediocre Mexican joint.

Pier 15 sounds great. Another Marin option that can work on the way to Mendo is Hilda's Coffee Shop in San Anselmo. Unpretentious as you can get, but good diner food, especially the German pancakes (thin and griddle-fried, unlike the baked kind).

Willow Wood is great also. If you don't want to go to the coast, it's a nice detour of its own. You can leave 101 in Santa Rosa, take River Road to Olivet Road, left on Olivet Road that takes you by some wineries, one being DeLoach (very good reds there) and other small ones, then right on Guerneville Road, left on Frey Road which becomes Graton Road and goes right to Graton. It's a not-long nice real-country drive. Then you can continue (after a turnaround and short hop to the Gravenstein Hwy) and go to Sebastopol, then on to 101. A map will make it clear. If you're up to the detour, Willow Wood is worth the experience. If not, Pier 15 in San Rafael is very good for breakfast (better than for lunch)..

I had a client in Ukiah and the SF through Santa Rosa traffic was really wearing. My trick for beating the traffic was to haul ass from SF to Hopland really early, then stop at Bluebird for a nice, leisurely breakfast and then do the last 25 minutes to Ukiah in time to arrive at 9am. Breakfast at Bluebird was the highlight of my day.

While all their food is good, Bluebird has the best chicken fried steak & eggs with biscuits & gravy that I've ever had in California and I KNOW my CFS and B&G.